High-throughput Sequencing Technologies

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2015 May 23

PMID 26000844

Citations 437

Authors

Jason A Reuter

Damek V Spacek

Michael P Snyder

Affiliations

Soon will be listed here.

Abstract

The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application.

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References

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G . The sequence of the human genome. Science. 2001; 291(5507):1304-51. DOI: 10.1126/science.1058040. View

Huang F, Hodis E, Xu M, Kryukov G, Chin L, Garraway L . Highly recurrent TERT promoter mutations in human melanoma. Science. 2013; 339(6122):957-9. PMC: 4423787. DOI: 10.1126/science.1229259. View

Schloss J . How to get genomes at one ten-thousandth the cost. Nat Biotechnol. 2008; 26(10):1113-5. DOI: 10.1038/nbt1008-1113. View

Smith M, Gianoulis T, Pukatzki S, Mekalanos J, Ornston L, Gerstein M . New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 2007; 21(5):601-14. PMC: 1820901. DOI: 10.1101/gad.1510307. View

Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A . Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93. PMC: 2858594. DOI: 10.1126/science.1181369. View

. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-14. PMC: 3564958. DOI: 10.1038/nature11234. View

Carneiro M, Russ C, Ross M, Gabriel S, Nusbaum C, DePristo M . Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics. 2012; 13:375. PMC: 3443046. DOI: 10.1186/1471-2164-13-375. View

Khalil A, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D . Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009; 106(28):11667-72. PMC: 2704857. DOI: 10.1073/pnas.0904715106. View

10.

Quick J, Quinlan A, Loman N . A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. Gigascience. 2014; 3:22. PMC: 4226419. DOI: 10.1186/2047-217X-3-22. View

11.

Wheeler D, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A . The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008; 452(7189):872-6. DOI: 10.1038/nature06884. View

12.

Turnbaugh P, Ley R, Mahowald M, Magrini V, Mardis E, Gordon J . An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122):1027-31. DOI: 10.1038/nature05414. View

13.

Rao S, Huntley M, Durand N, Stamenova E, Bochkov I, Robinson J . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665-80. PMC: 5635824. DOI: 10.1016/j.cell.2014.11.021. View

14.

Dohm J, Lottaz C, Borodina T, Himmelbauer H . Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008; 36(16):e105. PMC: 2532726. DOI: 10.1093/nar/gkn425. View

15.

Loomis E, Eid J, Peluso P, Yin J, Hickey L, Rank D . Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 2012; 23(1):121-8. PMC: 3530672. DOI: 10.1101/gr.141705.112. View

16.

Zhang Z, Du J, Lam H, Abyzov A, Urban A, Snyder M . Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011; 12:375. PMC: 3161018. DOI: 10.1186/1471-2164-12-375. View

17.

Bilguvar K, Ozturk A, Louvi A, Kwan K, Choi M, Tatli B . Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature. 2010; 467(7312):207-10. PMC: 3129007. DOI: 10.1038/nature09327. View

18.

Zhao J, Ohsumi T, Kung J, Ogawa Y, Grau D, Sarma K . Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 2010; 40(6):939-53. PMC: 3021903. DOI: 10.1016/j.molcel.2010.12.011. View

19.

Metzker M . Sequencing technologies - the next generation. Nat Rev Genet. 2009; 11(1):31-46. DOI: 10.1038/nrg2626. View

20.

Landt S, Marinov G, Kundaje A, Kheradpour P, Pauli F, Batzoglou S . ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012; 22(9):1813-31. PMC: 3431496. DOI: 10.1101/gr.136184.111. View